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Azam S, Zhu J, Jiang J, Wang J, Zhao H. Photolysis of dinotefuran in aqueous solution: Kinetics, influencing factors and photodegradation mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123352. [PMID: 38219898 DOI: 10.1016/j.envpol.2024.123352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
The environmental behaviour of neonicotinoid insecticides (NNIs) is of momentous concern due to their frequent detection in aquatic environment and their biotoxicity for non-target organisms. Phototransformation is one of the most significant transformation processes, which is directly related to NNIs exposure and environmental risks. In this study, the photodegradation of dinotefuran (DIN, 1-Methyl-2-nitro-3-(tetrahydro-3-furanylmethyl)-guanidine), one of the most promising NNIs, was conducted under irritated light in the presence of Cl-, DOM along with the effect of pH and initial concentration. The findings demonstrated that in ultra-pure (UP) water, the photolysis rate constants (k) of DIN rose with increasing initial concentration. Whereas, in tap water, at varied pH levels, and in the presence of Cl-, the outcomes were reversed. At the same time, lower concentration of DOM promoted DIN photolysis processes due to the production of reactive oxygen species, while higher concentrations of DOM inhibited the photolysis by the predominance of light shielding effects. The singlet oxygen (1O2) was produced in the photolysis processes of DIN with Cl- and DOM, which was confirmed by electron spin resonance (EPR) analysis. Four main photolysis products and three intermediates were identified by UPLC-Q-Exactive Orbitrap MS analysis. The possible photodegradation pathways of DIN were proposed including the oxidation by 1O2, reduction and hydrolysis after the removal of nitro group from parent compounds. This study expanding our understanding of transformation behavior and fate of NNIs in the aquatic environment, which is essential for estimating their environmental risks.
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Affiliation(s)
- Shafiul Azam
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
| | - Jie Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingqiu Jiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China.
| | - Jingyao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
| | - Hongxia Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
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2
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Li M, Zhu J, Lv Z, Qin H, Wang X, Shi H. Recent Advances in RNA-Targeted Cancer Therapy. Chembiochem 2024; 25:e202300633. [PMID: 37961028 DOI: 10.1002/cbic.202300633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/15/2023]
Abstract
Ribonucleic acid (RNA) plays a pivotal role in gene regulation and protein biosynthesis. Interfering the physiological function of key RNAs to induce cell apoptosis holds great promise for cancer treatment. Many RNA-targeted anti-cancer strategies have emerged continuously. Among them, RNA interference (RNAi) has been recognized as a promising therapeutic modality for various disease treatments. Nevertheless, the primary obstacle in siRNA delivery-escaping the endosome and crossing the plasma membrane severely impedes its therapeutic potential. Thus far, a variety of nanosystems as well as carrier-free bioconjugation for siRNA delivery have been developed and employed to enhance the drug delivery and anti-tumor efficiency. Besides, the use of small molecules to target specific RNA structures and disrupt their function, along with the covalent modification of RNA, has also drawn tremendous attention recently owing to high therapeutic efficacy. In this review, we will provide an overview of recent progress in RNA-targeted cancer therapy including various siRNA delivery strategies, RNA-targeting small molecules, and newly emerged covalent RNA modification. Finally, challenges and future perspectives faced in this research field will be discussed.
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Affiliation(s)
- Miao Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Jinfeng Zhu
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Roma, 00133, Italy
| | - Zhengzhong Lv
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Hongni Qin
- Suzhou Industrial Park Institute of Services Outsourcing, Suzhou, 215123, China
| | - Xiaoyan Wang
- Department of Ultrasound, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 046000, China
| | - Haibin Shi
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
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3
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Fang J, Liu Q, Liu Y, Li K, Qiu L, Xi H, Cai S, Zou P, Lin J. β-Galactosidase-Activated and Red Light-Induced RNA Modification Strategy for Prolonged NIR Fluorescence/PET Bimodality Imaging. Anal Chem 2024; 96:1707-1716. [PMID: 38241523 DOI: 10.1021/acs.analchem.3c04845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Improving the retention of small-molecule-based therapeutic agents in tumors is crucial to achieve precise diagnosis and effective therapy of cancer. Herein, we propose a β-galactosidase (β-Gal)-activated and red light-induced RNA modification (GALIRM) strategy for prolonged tumor imaging. A β-Gal-activatable near-infrared (NIR) fluorescence (FL) and positron emission tomography (PET) bimodal probe 68Ga-NOTA-FCG consists of a triaaza triacetic acid chelator NOTA for 68Ga-labeling, a β-Gal-activated photosensitizer CyGal, and a singlet oxygen (1O2)-susceptible furan group for RNA modification. Studies have demonstrated that the probe emits an activated NIR FL signal upon cleavage by endogenous β-Gal overexpressed in the lysosomes, which is combined with the PET imaging signal of 68Ga allowing for highly sensitive imaging of ovarian cancer. Moreover, the capability of 68Ga-NOTA-FCG generating 1O2 under 690 nm illumination could be simultaneously unlocked, which can trigger the covalent cross-linking between furan and nucleotides of cytoplasmic RNAs. The formation of the probe-RNA conjugate can effectively prevent exocytosis and prolong retention of the probe in tumors. We thus believe that this GALIRM strategy may provide entirely new insights into long-term tumor imaging and efficient tumor treatment.
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Affiliation(s)
- Jing Fang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Qingzhu Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Ke Li
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Ling Qiu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hongjie Xi
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Shuyue Cai
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Jianguo Lin
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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4
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Lu Z, Tan J, Wu Y, You J, Xie X, Zhang Z, Li Z, Chen L. NIR Light-Activated Mitochondrial RNA Cross-Linking Strategy for H 2S Monitoring and Prolonged Colorectal Tumor Imaging. Anal Chem 2023; 95:17089-17098. [PMID: 37940603 DOI: 10.1021/acs.analchem.3c04033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Molecular diffusion and leakage impede the long-term retention of probes/drugs and may cause potential adverse effects in theranostic fields. Spatiotemporally manipulating the organelle-immobilization behavior of probes/drugs for prolonged tumor retention is indispensable to achieving effective cancer diagnosis and therapy. Herein, we propose a rational strategy that could realize near-infrared light-activated ribonucleic acids (RNAs) cross-linking for prolonged tumor retention and simultaneously endogenous hydrogen sulfide (H2S) monitoring in colorectal tumors. Profiting from efficient singlet oxygen (1O2) generation from Cy796 under 808 nm light irradiation, the 1O2-animated furan moiety in Cy796 could covalently cross-link with cytoplasmic RNAs via a cycloaddition reaction and realize organelle immobilization. Subsequently, specific thiolysis of Cy796 assisted with H2S resulted in homologous product Cy644 with reduced 1O2 generation yields and enhanced absolute fluorescence quantum yields (from 7.42 to 27.70%) with blue-shifted absorption and emission, which avoided the molecular oxidation fluorescence quenching effect mediated by 1O2 and validated fluorescence imaging. Furthermore, studies have demonstrated that our proposed strategy possessed adequate capacity for fluorescence imaging and endogenous H2S detection in HCT116 cells, particularly accumulated at the tumor sites, and retained long-term imaging with excellent biocompatibility. The turn-on fluorescence mode and turn-off 1O2 generation efficiency in our strategy successfully realized a diminished fluorescence cross-talk and oxidation quenching effect. It is adequately envisioned that our proposed strategy for monitoring biomarkers and prolonged tumor retention will contribute tremendous dedication in the clinical, diagnostic, and therapeutic fields.
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Affiliation(s)
- Zhihao Lu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, P. R. China
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Jiangkun Tan
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, P. R. China
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, P. R. China
| | - Yuting Wu
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Jinmao You
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, P. R. China
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Xiunan Xie
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Zhiyong Zhang
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Zan Li
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai 264003, P. R. China
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5
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Zhang Q, Ali T, Lin Z, Peng X. Development of 4,4'-dibromobinaphthalene analogues with potent photo-inducible DNA cross-linking capability and cytotoxicity towards breast MDA-MB 468 cancer cells. Bioorg Chem 2023; 140:106769. [PMID: 37633128 DOI: 10.1016/j.bioorg.2023.106769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/25/2023] [Accepted: 08/06/2023] [Indexed: 08/28/2023]
Abstract
Photoinduced DNA cross-linking process showed advantages of high spatio-temporal resolution and control. We have designed, synthesized, and characterized several 4,4'-dibromo binaphthalene analogues (1a-f) that can be activated by 350 nm irradiation to induce various DNA damage, including DNA interstrand cross-links (ICL) formation, strand cleavages, and alkaline labile DNA lesions. The degree and types of DNA damage induced by these compounds depend on the leaving groups of the substrates, pH value of the buffer solution, and DNA sequences. The DNA ICL products were produced from the carbocations formed via the oxidation of free radicals photo-generated from 1a-f. Most of these compounds alone exhibited minimum cytotoxicity towards cancer cells while 350 nm irradiation greatly improved their anticancer effects (up to 40-fold enhancement) because of photo-induced cellular DNA damage. This work provides guidance for further design of photo-inducible DNA cross-linking agents as potent photo-activated anticancer prodrugs with good control over toxicity and selectivity.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Taufeeque Ali
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States.
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6
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Barr J, Colpaert G, Cadoni E, Madder A. Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting. Methods 2023; 218:189-197. [PMID: 37597698 DOI: 10.1016/j.ymeth.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Oligonucleotides (ODNs) find applications as diagnostic and therapeutic tools due to their unique ability to interact, thanks to Watson-Crick base pairing, with a specific DNA or RNA target strand. Although most of the tools available today rely on mere hydrogen bond formation, chemical modifications to enable covalent interstrand-crosslinking (ICL) have been reported, and are gaining a place under the spotlight as they potentially offer a series of advantages over the state of the art, including a higher potency and selectivity. This methodological paper focuses on the use of a pro-reactive furan moiety and its subsequent oxidation for applications in ODN targeting. The design of effective capture and targeting probes to ensure high ICL yields is discussed and the mechanisms underlying the (photo)chemical oxidation of furan are explained. Furthermore, examples of furan-containing DNAs designed for different applications, including DNA-DNA or DNA-RNA ICL and DNA-peptide/protein targeting, are provided. The paper highlights the advantages of using different oxidative chemical triggers, such as N-bromosuccinimide or singlet oxygen, to offer additional selectivity control over the ICL reaction.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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7
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De Paepe L, Cadoni E, Manicardi A, Madder A. Furan-modified PNA probes for covalent targeting and ligation of nucleic acids. Methods 2023; 218:210-223. [PMID: 37604247 DOI: 10.1016/j.ymeth.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
While natural oligonucleotides (ONs) are increasingly used as therapeutic and diagnostic tools, they still face certain challenges such as low resistance to enzymatic degradation, potential immunogenicity, and delivery issues, which can limit their applications. Peptide Nucleic Acids (PNAs) are promising alternatives due to their high affinity for DNA and RNA, the high resistance to enzymatic degradation, and the easy introduction of a wide range of potential modifications. Chemical modifications that enable the covalent targeting of specific DNA and RNA strands offer additional advantages, including enhanced potency. The current study focuses on the utilization of furan-PNAs as pro-reactive probe systems and their applications to DNA and RNA targeting. Specifically, in this methodological paper, we provide practical insights into the design, synthesis, and application of furan-containing PNA probes for achieving efficient PNA-DNA and PNA-RNA interstrand crosslinking (ICL), as well as ON-templated PNA-PNA ligation systems. Furthermore, we discuss the applications of these probes in targeting DNA secondary structures, such as G-quadruplexes and i-motifs, target pull-down assays, and on-surface detection.
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Affiliation(s)
- Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 17/A, I-43124 Parma, Italy.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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8
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Cadoni E, De Paepe L, Colpaert G, Tack R, Waegeman D, Manicardi A, Madder A. A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA. Nucleic Acids Res 2023; 51:4112-4125. [PMID: 36971129 PMCID: PMC10201448 DOI: 10.1093/nar/gkad189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/03/2023] [Accepted: 03/12/2023] [Indexed: 08/21/2023] Open
Abstract
The importance of non-canonical DNA structures such as G-quadruplexes (G4) and intercalating-motifs (iMs) in the fine regulation of a variety of cellular processes has been recently demonstrated. As the crucial roles of these structures are being unravelled, it is becoming more and more important to develop tools that allow targeting these structures with the highest possible specificity. While targeting methodologies have been reported for G4s, this is not the case for iMs, as evidenced by the limited number of specific ligands able to bind the latter and the total absence of selective alkylating agents for their covalent targeting. Furthermore, strategies for the sequence-specific covalent targeting of G4s and iMs have not been reported thus far. Herein, we describe a simple methodology to achieve sequence-specific covalent targeting of G4 and iM DNA structures based on the combination of (i) a peptide nucleic acid (PNA) recognizing a specific sequence of interest, (ii) a pro-reactive moiety enabling a controlled alkylation reaction, and (iii) a G4 or iM ligand orienting the alkylating warhead to the reactive residues. This multi-component system allows for the targeting of specific G4 or iM sequences of interest in the presence of competing DNA sequences and under biologically relevant conditions.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Ruben Tack
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Dries Waegeman
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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Neitz H, Bessi I, Kuper J, Kisker C, Höbartner C. Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition. J Am Chem Soc 2023; 145:9428-9433. [PMID: 37071840 DOI: 10.1021/jacs.3c01611] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (PhedU). The crosslinking ability of PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a PhedU dimer after short irradiation times of a few seconds. A PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Irene Bessi
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jochen Kuper
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, 97074 Würzburg, Germany
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10
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Fernández E, Miret-Casals L, Madder A, Gevaert K. Cell Surface Biotinylation Using Furan Cross-Linking Chemistry. Methods Mol Biol 2023; 2718:11-21. [PMID: 37665452 DOI: 10.1007/978-1-0716-3457-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
A detailed study of the cellular surfaceome poses major challenges for mass spectrometry analysis. Surface proteins are low abundant compared to intracellular proteins, and their inefficient extraction in aqueous medium leads to their aggregation and precipitation. To tackle such problems, surface biotinylation is frequently used to tag surface proteins with biotin, allowing for their enrichment, leading to a more sensitive mapping of surface proteomes. We here detail a new surface biotinylation protocol based on furan-biotin affinity purification to enrich plasma membrane proteins for proteomics. This protocol involves biotinylation of cell surface membrane proteins on viable cells, followed by affinity enrichment using streptavidin beads, trypsin digestion, peptide cleanup, and LC-MS/MS analysis.
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Affiliation(s)
- Esperanza Fernández
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laia Miret-Casals
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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11
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Fang J, Feng Y, Zhang Y, Wang A, Li J, Cui C, Guo Y, Zhu J, Lv Z, Zhao Z, Xu C, Shi H. Alkaline Phosphatase-Controllable and Red Light-Activated RNA Modification Approach for Precise Tumor Suppression. J Am Chem Soc 2022; 144:23061-23072. [DOI: 10.1021/jacs.2c10409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jing Fang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yali Feng
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yuqi Zhang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Anna Wang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jiachen Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Chaoxiang Cui
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Yirui Guo
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jinfeng Zhu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zhengzhong Lv
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zhongsheng Zhao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Chenjie Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR 999077, China
| | - Haibin Shi
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
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12
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Zhang Q, Lin Z, Peng X. Photo-Reactivity of Binaphthalene Triphenylphosphonium Salts: DNA Interstrand Cross-Link Formation and Substituent Effects. Chem Res Toxicol 2022; 35:1334-1343. [PMID: 35857929 DOI: 10.1021/acs.chemrestox.1c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Five novel 1,1'-binaphthalene analogues 1a-1e with triphenylphosphonium (TPP+) salts as a leaving group have been synthesized and characterized as photo-activatable DNA alkylating agents. Phototriggered release of the TPP+ group from 1a-1e generated naphthalenylmethyl-free radicals that were spontaneously transformed to the corresponding cations directly producing DNA interstrand cross-link (ICL) formation via alkylation. The substituents at position 4 not only affect the efficiency of ICL formation but also influence the reaction rate for DNA cross-linking. Groups with small or medium size favor ICL formation, while a bulky substituent (e.g., phenyl group) prevents DNA interstrand cross-linking. DNA alkylation by the naphthalenylmethyl cations photo-generated from 1a-1e occurs at dG, dC, and dA, while interstrand cross-linking took place with dG/dC base pairs. The TPP+ salts (1a-1e) are cations with both lipophilic and hydrophilic properties, which have great potential for biological applications.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin─Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin─Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin─Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
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13
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen PR. Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022; 61:e202202008. [DOI: 10.1002/anie.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Huixin Luo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines Institute of Materia Medica Chinese Academy of Medical Sciences and Peking UnionMedical College Beijing 100050 China
| | - Wei Tang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Hongyu Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - William Shu Ching Ngai
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Rui Gao
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Heyun Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Ran Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianting Guo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Fangfei Qin
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Gang Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Kexin Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Xinyuan Fan
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
| | - Peng R. Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
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14
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Singh A, Bhatia D. DNA Nanotechnology-Based Supramolecular Assemblies for Targeted Biomedical Applications. CHEM REC 2022; 22:e202200048. [PMID: 35532197 DOI: 10.1002/tcr.202200048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/24/2022] [Indexed: 11/10/2022]
Abstract
DNA is a polyanionic, hydrophilic, and natural biopolymer that offers properties such as biodegradability, biocompatibility, non-toxicity, and non-immunogenicity. These properties of DNA as an ideal biopolymer offer modern-day researchers' reasons to exploit these to form high-order supramolecular assemblies. These structures could range from simple to complex and provide various applications. Among them, supramolecular assemblies like DNA hydrogels (DNA-HG) and DNA dendrimers (DNA-DS) show massive growth potential in the areas of biomedical applications such as cell biology, medical stream, molecular biology, pharmacology, and healthcare product manufacturing. The application of both of these assemblies has seen enormous growth in recent years. In this focused review on DNA-based supramolecular assemblies like hydrogels and dendrimers, we present the principles of synthesis and characterization, key developments with examples and applications, and conclude with a brief perspective on challenges and future outlook for such devices and their subsequent applications.
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Affiliation(s)
- Ankur Singh
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India E-mail: Dhiraj Bhatia
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India E-mail: Dhiraj Bhatia.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
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15
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen P. Photocatalytic Chemical Crosslinking for Profiling RNA‐Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huixin Luo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Wei Tang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Hongyu Liu
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiangmei Zeng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | | | - Rui Gao
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Heyun Li
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Ran Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Huangtao Zheng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jianting Guo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fangfei Qin
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Gang Wang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Kexin Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Xinyuan Fan
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Zou
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Chen
- Peking University tional Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering 100871 Beijing CHINA
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16
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Aerssens D, Cadoni E, Tack L, Madder A. A Photosensitized Singlet Oxygen ( 1O 2) Toolbox for Bio-Organic Applications: Tailoring 1O 2 Generation for DNA and Protein Labelling, Targeting and Biosensing. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030778. [PMID: 35164045 PMCID: PMC8838016 DOI: 10.3390/molecules27030778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
Singlet oxygen (1O2) is the excited state of ground, triplet state, molecular oxygen (O2). Photosensitized 1O2 has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of 1O2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of 1O2, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring 1O2 generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor 1O2 generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.
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17
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Pierau L, Elian C, Akimoto J, Ito Y, Caillol S, Versace DL. Bio-sourced Monomers and Cationic Photopolymerization: The Green combination towards Eco-Friendly and Non-Toxic Materials. Prog Polym Sci 2022. [DOI: 10.1016/j.progpolymsci.2022.101517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Cadoni E, Pennati F, Muangkaew P, Elskens J, Madder A, Manicardi A. Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown. RSC Chem Biol 2022; 3:1129-1143. [PMID: 36128507 PMCID: PMC9428673 DOI: 10.1039/d2cb00095d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
After optimization of interstrand crosslink reaction between furan-containing peptide nucleic acids and target oligonucleotides, the reversibility of the formed product is exploited for the pull-down of a sequence of interest from cell lysates.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Francesca Pennati
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, 10330 Bangkok, Thailand
| | - Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
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19
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Singh A, Bhatia D. DNA hydrogels: Principles, synthesis, characterization and applications to cell biology. Methods Cell Biol 2022; 169:323-346. [DOI: 10.1016/bs.mcb.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Liu W, Watson EE, Winssinger N. Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
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21
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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22
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Nowak-Karnowska J, Zielińska K, Milecki J, Skalski B. Thermally reversible and irreversible interstrand photocrosslinking of 5-chloro-2'-deoxy-4-thiouridine modified DNA oligonucleotides. Org Biomol Chem 2021; 19:1292-1295. [PMID: 33508059 DOI: 10.1039/d0ob02422h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe highly efficient interstrand photocrosslinking of a DNA duplex containing 5-chloro-2'-deoxy-4-thiouridine (ClSdU) in one strand, proceeding via a two-step photochemical cascade, involving the formation of a thermally reversible crosslink between ClSdU and thymidine in the target strand and its subsequent conversion to a thermally stable fluorescent crosslink. These results show that ClSdU has great potential to be a valuable DNA photo-crosslinking reagent for chemical biology applications.
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Affiliation(s)
- Joanna Nowak-Karnowska
- Department of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland.
| | - Karolina Zielińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jan Milecki
- Department of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland.
| | - Bohdan Skalski
- Department of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland. and Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614 Poznań, Poland
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23
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Abdelhady AM, Hirano Y, Onizuka K, Okamura H, Komatsu Y, Nagatsugi F. Synthesis of crosslinked 2'-OMe RNA duplexes and their application for effective inhibition of miRNA function. Bioorg Med Chem Lett 2021; 48:128257. [PMID: 34246752 DOI: 10.1016/j.bmcl.2021.128257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022]
Abstract
The interstrand crosslinking of nucleic acids is one of the strategies to create the stable complex between an oligonucleotide and RNA by covalent bond formation. We previously reported that fully 2'-O-methylated (2'-OMe) RNAs having the 2-amino-6-vinylpurine (AVP) exhibited an efficient crosslinking to uracil in the target RNA. In this study, we established a chemical method to efficiently synthesize the crosslinked 2'-OMe RNA duplexes using AVP and prepared the anti-miRNA oligonucleotides (AMOs) containing the antisense targeting miR-21 and crosslinked duplex at the terminal sequences. These AMOs showed a markedly higher anti miRNA activity than that of the commercially-available miR-21 inhibitor which has locked nucleic acid (LNA) residues.
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Affiliation(s)
- Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884 Cairo, Egypt
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
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24
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Miret-Casals L, Vannecke W, Hoogewijs K, Arauz-Garofalo G, Gay M, Díaz-Lobo M, Vilaseca M, Ampe C, Van Troys M, Madder A. Furan warheads for covalent trapping of weak protein-protein interactions: cross-linking of thymosin β4 to actin. Chem Commun (Camb) 2021; 57:6054-6057. [PMID: 34036992 DOI: 10.1039/d1cc01731d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe furan as a triggerable 'warhead' for site-specific cross-linking using the actin and thymosin β4 (Tβ4)-complex as model of a weak and dynamic protein-protein interaction (PPI) with known 3D structure and with application potential in disease contexts. The identified cross-linked residues demonstrate that lysine is a target for the furan warhead. The presented in vitro validation of covalently acting 'furan-armed' Tβ4-variants provides initial proof to further exploit furan-technology for covalent drug design targeting lysines.
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Affiliation(s)
- Laia Miret-Casals
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281 S4, Ghent B-9000, Belgium.
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25
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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26
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Interrogating biological systems using visible-light-powered catalysis. Nat Rev Chem 2021; 5:322-337. [PMID: 37117838 DOI: 10.1038/s41570-021-00265-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Light-powered catalysis has found broad utility as a chemical transformation strategy, with widespread impact on energy, environment, drug discovery and human health. A noteworthy application impacting human health is light-induced sensitization of cofactors for photodynamic therapy in cancer treatment. The clinical adoption of this photosensitization approach has inspired the search for other photochemical methods, such as photoredox catalysis, to influence biological discovery. Over the past decade, light-mediated catalysis has enabled the discovery of valuable synthetic transformations, propelling it to become a highly utilized chemical synthesis strategy. The reaction components required to achieve a photoredox reaction are identical to photosensitization (catalyst, light source and substrate), making it ideally suited for probing biological environments. In this Review, we discuss the therapeutic application of photosensitization and advancements made in developing next-generation catalysts. We then highlight emerging uses of photoredox catalytic methods for protein bioconjugation and probing complex cellular environments in living cells.
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27
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Fan H, Sun H, Zhang Q, Peng X. Photoinduced DNA Interstrand Cross-Linking by 1,1'-Biphenyl Analogues: Substituents and Leaving Groups Combine to Determine the Efficiency of Cross-Linker. Chemistry 2021; 27:5215-5224. [PMID: 33440025 DOI: 10.1002/chem.202005064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/05/2021] [Indexed: 11/11/2022]
Abstract
Two series of 1,1'-biphenyl analogues with various leaving groups (L=OAc, OCH3 , OCHCH=CH2 , OCH2 Ph, SPh, SePh, and Ph3 P+ ) were synthesized. Their reactivity towards DNA and the reaction mechanism were investigated by determining DNA interstrand cross-link (ICL) efficiency, radical and carbocation formation, and the cross-linking reaction sites. All compounds induced DNA ICL formation upon 350 nm irradiation via a carbocation that was generated from oxidation of the corresponding free radicals. The ICL efficiency and the reaction rate strongly depended on the combined effect of the leaving group and the substituent. Among all compounds tested, the high ICL efficiency (30-43 %) and fast reaction rate were observed with compounds carrying a nitrophenyl group and acetate (2 a), ether (2 b and 2 c), or triphenylphosphonium salt (2 g) as leaving groups. Most compounds with a 4-methoxybenzene group showed similar DNA ICL efficiency (≈30 %) with a slow DNA cross-linking reaction rate. Both cation trapping and free radical trapping adducts were detected in the photo activation process of these compounds, which provided direct evidence for the proposed mechanism. Heat stability study in combination with sequence study suggested that these photo-generated benzyl cations alkylate DNA at dG, dA, and dC sites.
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Affiliation(s)
- Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Huabing Sun
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA
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28
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De Geyter E, Antonatou E, Kalaitzakis D, Smolen S, Iyer A, Tack L, Ongenae E, Vassilikogiannakis G, Madder A. 5-Hydroxy-pyrrolone based building blocks as maleimide alternatives for protein bioconjugation and single-site multi-functionalization. Chem Sci 2021; 12:5246-5252. [PMID: 34163760 PMCID: PMC8179572 DOI: 10.1039/d0sc05881e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/15/2021] [Indexed: 11/23/2022] Open
Abstract
Recent dramatic expansion in potential uses of protein conjugates has fueled the development of a wide range of protein modification methods; however, the desirable single-site multi-functionalization of proteins has remained a particularly intransigent challenge. Herein, we present the application of 5-hydroxy-1,5-dihydro-2H-pyrrol-2-ones (5HP2Os) as advantageous alternatives to widely used maleimides for the chemo- and site-selective labeling of cysteine residues within proteins. A variety of 5HP2O building blocks have been synthesized using a one-pot photooxidation reaction starting from simple and readily accessible furans and using visible light and oxygen. These novel reagents display excellent cysteine selectivity and also yield thiol conjugates with superior stability. 5HP2O building blocks offer a unique opportunity to introduce multiple new functionalities into a protein at a single site and in a single step, thus, significantly enhancing the resultant conjugate's properties.
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Affiliation(s)
- Ewout De Geyter
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Eirini Antonatou
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Dimitris Kalaitzakis
- Department of Chemistry, University of Crete Vasilika Vouton 71003 Iraklion Crete Greece
| | - Sabina Smolen
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Abhishek Iyer
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Laure Tack
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Emiel Ongenae
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | | | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group OBCR, Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
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29
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Truong VX, Barner-Kowollik C. Red-Light Driven Photocatalytic Oxime Ligation for Bioorthogonal Hydrogel Design. ACS Macro Lett 2021; 10:78-83. [PMID: 35548995 DOI: 10.1021/acsmacrolett.0c00767] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Light-mediated polymer cross-linking is frequently employed for the preparation of hydrogels for biomedical applications. However, most photopolymerization processes require activation by UV light or short wavelength visible light, which are highly absorbed by skin and tissue, limiting their uses in transdermal initiation. Herein, we introduce red light-enabled oxime ligation by the in situ photogeneration of aldehydes, which rapidly react with hydroxylamines. We demonstrate efficient polymer cross-linking behind a dermal tissue model by red light initiation. Optimization of the photopolymerization conditions allows for 3D encapsulation of human foreskin fibroblasts with good cell viability postencapsulation.
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Affiliation(s)
- Vinh X. Truong
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane 4000, Australia
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane 4000, Australia
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30
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Cadoni E, Manicardi A, Fossépré M, Heirwegh K, Surin M, Madder A. Teaching photosensitizers a new trick: red light-triggered G-quadruplex alkylation by ligand co-localization. Chem Commun (Camb) 2021; 57:1010-1013. [PMID: 33404017 DOI: 10.1039/d0cc06030e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We propose a bimolecular approach for G-quadruplex alkylation, using a pro-reactive furan-containing ligand, activated by red-light irradiation of a proximate G4-binding photosensitizer. G4- over dsDNA alkylation can be achieved selectively and proves high-yielding at low ligand excess. HPLC and modelling studies allowed identifying potential residues involved in the alkylation.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Research Group, Faculty of Sciences, University of Ghent Campus Sterre, Krijgslaan 281, Building S4, B-9000 Gent, Belgium.
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31
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Fan H, Peng X. Photoinduced DNA Interstrand Cross-Linking by Benzene Derivatives: Leaving Groups Determine the Efficiency of the Cross-Linker. J Org Chem 2021; 86:493-506. [PMID: 33253574 DOI: 10.1021/acs.joc.0c02234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We have synthesized and characterized two small libraries of 2-OMe or 2-NO2-benzene analogues 2a-i and 3a-i containing a wide variety of leaving groups. Irradiation of these compounds at 350 nm generated benzyl radicals that were spontaneously oxidized to benzyl cations directly producing DNA interstrand cross-links (ICLs). Compounds with a 2-methoxy substituent showed a faster cross-linking reaction rate and higher ICL efficiency than the corresponding 2-nitro analogues. Apart from the aromatic substituent, the benzylic leaving groups greatly affected DNA cross-linking efficiency. Higher ICL yields were observed for compounds with OCH3 (3b), OCH2Ph (3d), or Ph3P+ (3i) as leaving groups than those containing OAc (3a), NMe2 (3e), morpholine (3f), OCH2CH═CH2 (3c), SPh (3g), or SePh (3h). The heat stability study of the isolated ICL products indicated that dGs were the preferred alkylation sites in DNA for the benzyl cations produced from 2a-i, 3c, and 3e-i while 3a (L = OAc), 3b (L = OMe), and 3d (L = OCH2Ph) showed a similar photoreactivity toward dGs and dAs. Although the photogenerated benzyl cations alkylated dG, dC, and dA, ICL assay with variation of DNA sequences showed that the ICL reaction occurred with opposing dG/dC but not with staggered dA/dA.
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Affiliation(s)
- Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin 53211, United States
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32
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Ye S, Cui C, Cheng X, Zhao M, Mao Q, Zhang Y, Wang A, Fang J, Zhao Y, Shi H. Red Light-Initiated Cross-Linking of NIR Probes to Cytoplasmic RNA: An Innovative Strategy for Prolonged Imaging and Unexpected Tumor Suppression. J Am Chem Soc 2020; 142:21502-21512. [PMID: 33306393 DOI: 10.1021/jacs.0c10755] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Improving the enrichment of drugs or theranostic agents within tumors is very vital to achieve effective cancer diagnosis and therapy while greatly reducing the dosage and damage to normal tissues. Herein, as a proof of concept, we for the first time report a red light-initiated probe-RNA cross-linking (RLIPRC) strategy that can not only robustly promote the accumulation and retention of the probe in the tumor for prolonged imaging but also significantly inhibits the tumor growth. A near-infrared (NIR) fluorescent probe f-CR consisting of a NIR dye (Cyanine 7) as a signal reporter, a cyclic-(arginine-glycine-aspartic acid) (cRGD) peptide for tumor targeting, and a singlet oxygen (1O2)-sensitive furan moiety for RNA cross-linking was rationally designed and synthesized. This probe possessed both passive and active tumor targeting abilities and emitted intense NIR/photoacoustic (PA) signals, allowing for specific and sensitive dual-modality imaging of tumors in vivo. Notably, probe f-CR could be specifically and covalently cross-linked to cytoplasmic RNAs via the cycloaddition reaction between furan and adenine, cytosine, or guanine under the oxidation of 1O2 generated in situ by irradiation of methylene blue (MB) with 660 nm laser light, which effectively blocks the exocytosis of the probes resulting in enhanced tumor accumulation and retention. More excitingly, for the first time, we revealed that the covalent cross-linking of probe f-CR to cytoplasmic RNAs could induce severe apoptosis of cancer cells leading to remarkable tumor suppression. This study thus represents the first red light-initiated RNA cross-linking system with high potential to improve the diagnostic and therapeutic outcomes of tumors in vivo.
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Affiliation(s)
- Shuyue Ye
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Chaoxiang Cui
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Xiaju Cheng
- Jiangsu Key Laboratory of Infection & Immunity, Institutes of Biology & Medical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Meng Zhao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Qiulian Mao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Yuqi Zhang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Anna Wang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Jing Fang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Yan Zhao
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Haibin Shi
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
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33
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Muangkaew P, Vilaivan T. Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency. Chembiochem 2020; 22:241-252. [PMID: 32889765 DOI: 10.1002/cbic.202000589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/03/2020] [Indexed: 12/27/2022]
Abstract
In this study, we describe a furan-modified acpcPNA as a probe that can form an interstrand crosslink (ICL) with its DNA target upon activation with N-bromosuccinimide (NBS). To overcome the problem of furan instability under acidic conditions, a simple and versatile post-synthetic methodology for the attachment of the furan group to the PNA probe was developed. Unlike in other designs, the furan was placed at the end of the PNA molecule or tethered to the PNA backbone with all the base pairs in the PNA ⋅ DNA duplexes fully preserved. Hence, the true reactivity of each nucleobase towards the crosslinking could be compared. We show that all DNA bases except T could participate in the crosslinking reaction when the furan was placed at the end of the PNA strand. The crosslinking process was sensitive to mispairing, and lower crosslinking efficiency was observed in the presence of a base-mismatch in the PNA ⋅ DNA duplex. In contrast, when the furan was placed at internal positions of the acpcPNA ⋅ DNA duplex, no ICL was observed; this was explained by the inability of a hydrogen-bonded nucleobase to participate in the crosslinking reaction. The crosslinking efficiency was considerably improved, despite lower duplex stability, when an unpaired base (in the form of C-insertion) was present in the complementary DNA strand close to the furan modification site.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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34
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Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
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Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
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35
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36
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Kikuta K, Taniguchi Y, Sasaki S. Study of the Inducible Cross-Linking Reaction to mRNA and the Effect on the Translation. Chem Pharm Bull (Tokyo) 2019; 67:877-883. [PMID: 31366836 DOI: 10.1248/cpb.c19-00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 4-vinylpyrimidin-2-one nucleoside (T-vinyl) forms a cross-link with the RNA containing uracil at the complementary site at a high reaction rate. To obtain the stable T-vinyl derivative so that its reactivity is protected until it access to the target site, several derivatives were investigated, and the 2-thiopyridinyl- and 2-thiopyrimidinyl T-vinyl derivatives were determined to be good candidates. The 2-thiopyrimidinyl T-vinyl derivative was found to more efficiently cross-link with mRNA albeit having a better stability than the 2-thiopyridinyl T-vinyl derivative. The investigation using the luciferase (Luc) mRNA, the synthetic mRNA and non-cellular translation system revealed that the translation is terminated at the end of the cross-linked duplex between the mRNA and the oligoribonucleotide (ORN). Thus, the 2-thiopyrimidinyl T-vinyl derivative has successfully demonstrated both a good stability and high efficiency for the cross-linking reaction, and expanded its applicability in biological applications.
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Affiliation(s)
- Kenji Kikuta
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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37
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Furan Cross-Linking Technology for Investigating GPCR-Ligand Interactions. Methods Mol Biol 2019. [PMID: 30969412 DOI: 10.1007/978-1-4939-9121-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Interactions between G protein-coupled receptors and their ligands hold extensive potential for drug discovery. Studying these interactions poses technical problems due to their transient nature and the inherent difficulties when working with G protein-coupled receptors (GPCR) that are only functional in a membrane setting. Here, we describe the use of a furan-based chemical cross-linking methodology to achieve selective covalent coupling between a furan-modified peptide ligand and its native GPCR present on the surface of living cells under normal cell culture conditions. This methodology relies on the oxidation of the furan moiety, which can be achieved by either addition of an external oxidation signal or by the reactive oxygen species produced by the cell. The cross-linked ligand-GPCR complex is subsequently detected by Western blotting based on the biotin label that is incorporated in the peptide ligand.
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38
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Rozelle AL, Kumar RN, Lee S. Photo-induced DNA interstrand cross-links formed by a coumarin-modified nucleoside. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:236-247. [PMID: 30922158 DOI: 10.1080/15257770.2018.1515439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Coumarins are a class of naturally occurring compounds that have been shown to form photochemical DNA interstrand cross-links (ICLs). However, study of a coumarin base has not been explored. Using nucleophilic substitution and phosphoramidite chemistry, we synthesized a coumarin base-containing oligonucleotide. Upon exposure to long-wave ultraviolet light, the coumarin-modified oligonucleotide formed ICLs with complementary oligonucleotide containing dT and dC opposite the coumarin base, presumably through a [2 + 2] cycloaddition mechanism. Moderate yields with both bases were observed; though, dT has a higher reactivity than dC. Overall, this work provides new means for biochemical characterization of ICLs formed by coumarins.
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Affiliation(s)
- Aaron Leland Rozelle
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
| | - Rayala Naveen Kumar
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
| | - Seongmin Lee
- a Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy, The University of Texas at Austin , Austin , Texas , 78712 , USA
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Muthmann N, Muttach F, Rentmeister A. Enzymatic Transfer of Photo-Cross-Linkers for RNA-Protein Photo-Cross-Linking at the mRNA 5'-Cap. Methods Mol Biol 2019; 2008:131-146. [PMID: 31124094 DOI: 10.1007/978-1-4939-9537-0_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Photo-cross-linking moieties have proven invaluable for elucidating interactions of biomolecules. While methods for site-specific incorporation of those moieties into proteins have been developed, comparable methods for nucleic acids are lacking. Utilizing the inherent specificity of enzymes, methyltransferases (MTase) exhibiting relaxed cosubstrate specificity in combination with synthetic analogs of S-adenosyl-L-methionine (AdoMet) allow for the precise installation of reporter molecules or affinity tags in various biomolecules. In this chapter, we describe AdoMet analogs with photo-cross-linking moieties that-in combination with an MTase-are ideal for site-specific installation. The workflow for chemo-enzymatic installation of photo-cross-linking moieties at the mRNA cap based on AdoMet analogs is given in detail.
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Affiliation(s)
- Nils Muthmann
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany
| | - Fabian Muttach
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Muenster, Münster, Germany.
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40
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De Laet N, Llamas EM, Madder A. Templated DNA Cross-Linking: Towards a Non-Invasive Singlet-Oxygen-Based Triggering Method. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201700175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nathalie De Laet
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Eva M. Llamas
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
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41
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Almeida-Marrero V, van de Winckel E, Anaya-Plaza E, Torres T, de la Escosura A. Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management. Chem Soc Rev 2018; 47:7369-7400. [DOI: 10.1039/c7cs00554g] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present article reviews the most important developing strategies in light-induced nanomedicine, based on the combination of porphyrinoid photosensitizers with a wide variety of biomolecules and biomolecular assemblies.
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Affiliation(s)
| | | | - Eduardo Anaya-Plaza
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
- Institute for Advanced Research in Chemistry (IAdChem)
| | - Andrés de la Escosura
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
- Institute for Advanced Research in Chemistry (IAdChem)
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42
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Vannecke W, Ampe C, Van Troys M, Beltramo M, Madder A. Cross-Linking Furan-Modified Kisspeptin-10 to the KISS Receptor. ACS Chem Biol 2017; 12:2191-2200. [PMID: 28714670 DOI: 10.1021/acschembio.7b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical cross-linking is well-established for investigating protein-protein interactions. Traditionally, photo cross-linking is used but is associated with problems of selectivity and UV toxicity in a biological context. We here describe, with live cells and under normal growth conditions, selective cross-linking of a furan-modified peptide ligand to its membrane-presented receptor with zero toxicity, high efficiency, and spatio-specificity. Furan-modified kisspeptin-10 is covalently coupled to its glycosylated membrane receptor, GPR54(KISS1R). This newly expands the applicability of furan-mediated cross-linking not only to protein-protein cross-linking but also to cross-linking in situ. Moreover, in our earlier reports on nucleic acid interstrand cross-linking, furan activation required external triggers of oxidation (via addition of N-bromo succinimide or singlet oxygen). In contrast, we here show, for multiple cell lines, the spontaneous endogenous oxidation of the furan moiety with concurrent selective cross-link formation. We propose that reactive oxygen species produced by NADPH oxidase (NOX) enzymes form the cellular source establishing furan oxidation.
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Affiliation(s)
- Willem Vannecke
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Christophe Ampe
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Marleen Van Troys
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Massimiliano Beltramo
- Equipe
Neuroendocrinologie Moleculaire de la Reproduction, Physiologie de
la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Annemieke Madder
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
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43
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Muttach F, Mäsing F, Studer A, Rentmeister A. New AdoMet Analogues as Tools for Enzymatic Transfer of Photo-Cross-Linkers and Capturing RNA-Protein Interactions. Chemistry 2017; 23:5988-5993. [PMID: 28042932 DOI: 10.1002/chem.201605663] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Indexed: 11/06/2022]
Abstract
Elucidation of biomolecular interactions is of utmost importance in biochemistry. Photo-cross-linking offers the possibility to precisely determine RNA-protein interactions. However, despite the inherent specificity of enzymes, approaches for site-specific introduction of photo-cross-linking moieties into nucleic acids are scarce. Methyltransferases in combination with synthetic analogues of their natural cosubstrate S-adenosyl-l-methionine (AdoMet) allow for the post-synthetic site-specific modification of biomolecules. We report on three novel AdoMet analogues bearing the most widespread photo-cross-linking moieties (aryl azide, diazirine, and benzophenone). We show that these photo-cross-linkers can be enzymatically transferred to the methyltransferase target, that is, the mRNA cap, with high efficiency. Photo-cross-linking of the resulting modified mRNAs with the cap interacting protein eIF4E was successful with aryl azide and diazirine but not benzophenone, reflecting the affinity of the modified 5' caps.
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Affiliation(s)
- Fabian Muttach
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Florian Mäsing
- University of Münster, Department of Chemistry, Institute of Organic Chemistry, Corrensstr. 40, 48149, Münster, Germany
| | - Armido Studer
- University of Münster, Department of Chemistry, Institute of Organic Chemistry, Corrensstr. 40, 48149, Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Germany
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44
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Llamas EM, Tome JPC, Rodrigues JMM, Torres T, Madder A. Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking. Org Biomol Chem 2017. [DOI: 10.1039/c7ob01269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.
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Affiliation(s)
- Eva M. Llamas
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
- Departamento de Química Orgánica
| | - João P. C. Tome
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - João M. M. Rodrigues
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Imdea-Nanoscience
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
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45
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Novel mitochondria-targeted, nitrogen mustard-based DNA alkylation agents with near infrared fluorescence emission. Talanta 2016; 161:888-893. [DOI: 10.1016/j.talanta.2016.08.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 11/23/2022]
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46
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Guo C, Asamitsu S, Kashiwazaki G, Sato S, Bando T, Sugiyama H. DNA Interstrand Crosslinks by H-pin Polyamide (S
)-seco
-CBI Conjugates. Chembiochem 2016; 18:166-170. [DOI: 10.1002/cbic.201600425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Chuanxin Guo
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwakecho Sakyo-ku Kyoto Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo-ku Kyoto Japan
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47
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Wang Y, Liu S, Lin Z, Fan Y, Wang Y, Peng X. Photochemical Generation of Benzyl Cations That Selectively Cross-Link Guanine and Cytosine in DNA. Org Lett 2016; 18:2544-7. [PMID: 27191599 PMCID: PMC5609456 DOI: 10.1021/acs.orglett.6b00755] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV irradiation of several aryl boronates efficiently produced bifunctional benzyl cations that selectively form guanine-cytosine cross-links in DNA. Photoinduced homolysis of the C-Br bond took place with the aryl boronate bromides 3a and 4a, generating free radicals that were oxidized to benzyl cations via electron transfer. However, photoirradiation of the quaternary ammonium salts 3b and 4b led to heterolysis of C-N bond, directly producing benzyl cations. The electron-donating group in the aromatic ring greatly enhanced cross-linking efficiency.
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Affiliation(s)
- Yibin Wang
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Shuo Liu
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yukai Fan
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and Milwaukee Institute of Drug Discovery, University of Wisconsin Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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48
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Manicardi A, Gyssels E, Corradini R, Madder A. Furan-PNA: a mildly inducible irreversible interstrand crosslinking system targeting single and double stranded DNA. Chem Commun (Camb) 2016; 52:6930-3. [PMID: 27147261 DOI: 10.1039/c6cc02062c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We here report on the design and synthesis of tailor-made furan-modified peptide nucleic acid (PNA) probes for covalent targeting of single stranded DNA through a crosslinking strategy. After introducing furan-containing building blocks into a PNA sequence, hybridization and furan-oxidation based crosslinking to DNA is investigated. The structure of the crosslinked products is characterized and preliminary investigations concerning the application of these systems to double stranded DNA are shown.
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Affiliation(s)
- A Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy.
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49
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Antonatou E, Hoogewijs K, Kalaitzakis D, Baudot A, Vassilikogiannakis G, Madder A. Singlet Oxygen-Induced Furan Oxidation for Site-Specific and Chemoselective Peptide Ligation. Chemistry 2016; 22:8457-61. [PMID: 27113264 DOI: 10.1002/chem.201601113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 01/06/2023]
Abstract
A novel chemoselective ligation methodology has been developed for the facile construction of peptide-based fluorescent probes. Furan-containing peptides were activated by singlet oxygen and covalently engaged by nitrogen nucleophiles to yield stable conjugates. Singlet oxygen was compatible with sensitive amino acid residues within the peptides and a range of fluorophores, bearing different functionalities, were successfully incorporated, illustrating the broad scope of the developed strategy.
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Affiliation(s)
- Eirini Antonatou
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Gent, Belgium
| | - Kurt Hoogewijs
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Gent, Belgium.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dimitris Kalaitzakis
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003, Iraklion, Crete, Greece
| | - Andreas Baudot
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Gent, Belgium
| | | | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000, Gent, Belgium.
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50
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De Laet N, Madder A. Synthesis and evaluation of methylene blue oligonucleotide conjugates for DNA interstrand cross-linking. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.11.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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